Test additional tag fix by mvdbeek · Pull Request #23 · mvdbeek/galaxy

mvdbeek · 2022-03-17T10:53:52Z

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We need the exit code in the metadata script to figure out the correct job messages. This would fix ``` FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_1] FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_2] FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_3] FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_5] FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_9] FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_10] ``` that are broken when using `metadata_strategy: extended` (galaxyproject#13551).

Fixes ``` FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_grooming FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_posixlines FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_spaces_to_tabs ```

xref: galaxyproject#13551, fixes ``` galaxy.jobs ERROR 2022-03-15 00:21:29,515 [pN:main,p:2180,tN:LocalRunner.work_thread-3] problem importing job outputs. stdout [] stderr [ Traceback (most recent call last): File "metadata/set.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 121, in set_metadata set_metadata_portable() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 291, in set_metadata_portable collect_dynamic_outputs(job_context, output_collections) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/job_execution/output_collect.py", line 147, in collect_dynamic_outputs persist_elements_to_hdca(job_context, elements, hdca, collector=DEFAULT_DATASET_COLLECTOR) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 719, in persist_elements_to_hdca filenames, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 292, in populate_collection_elements final_job_state=final_job_state, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 354, in _populate_elements self.add_tags_to_datasets(datasets=element_datasets["datasets"], tag_lists=element_datasets["tag_lists"]) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 576, in add_tags_to_datasets self.tag_handler.add_tags_from_list(user, dataset, tags, flush=False) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 61, in add_tags_from_list return self.set_tags_from_list(user, item, new_tags_set, flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 75, in set_tags_from_list self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 207, in apply_item_tags self.apply_item_tag(user, item, name, value, flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 179, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 281, in _get_or_create_tag tag = self._create_tag(scrubbed_tag_str) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 246, in _create_tag tag = self._create_tag_instance(tag_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 428, in _create_tag_instance tag = super()._create_tag_instance(tag_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 259, in _create_tag_instance Session = sessionmaker(self.sa_session.bind) AttributeError: 'NoneType' object has no attribute 'bind' ] Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish import_model_store.perform_import(history=job.history, job=job) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import datasets_attrs = self.datasets_properties() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties datasets_attrs = load(open(datasets_attrs_file_name)) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt' galaxy.jobs.runners ERROR 2022-03-15 00:21:29,516 [pN:main,p:2180,tN:LocalRunner.work_thread-3] (7/) Job wrapper finish method failed Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/__init__.py", line 594, in _finish_or_resubmit_job job_stderr=job_stderr, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish import_model_store.perform_import(history=job.history, job=job) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import datasets_attrs = self.datasets_properties() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties datasets_attrs = load(open(datasets_attrs_file_name)) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt' ```

mvdbeek · 2022-03-17T10:54:46Z

/api env_vars="GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true"

mvdbeek · 2022-03-17T11:05:25Z

/api env_vars="GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true"

mvdbeek · 2022-03-17T11:09:08Z

/api env_vars="GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true"

mvdbeek added 6 commits March 17, 2022 10:38

Drop redundant exit_code_path writing from DEFAULT_JOB_FILE_TEMPLATE.sh

056d254

Fix path to exit_code file

5d84c98

Add missing return statement in get_tag_by_name

18e4ec2

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Test additional tag fix#23

Test additional tag fix#23
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test_additional_tag_fix

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mvdbeek commented Mar 17, 2022

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